In [1]:
! pip install plotly==5.6.0
! pip install "notebook>=5.3" "ipywidgets>=7.5"

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In [2]:
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
from plotly import graph_objs as go
In [3]:
brain_d = pd.read_csv("./data/kirby21AllLevels.csv", header = 0)
brain_d = brain_d.drop(brain_d.columns[0], axis = 1)
brain_d.head()
Out[3]:
rawid roi volume min max mean std type level id icv tbv
0 kirby127a_3_1_ax.img Telencephalon_L 531111 0.0 374.0 128.3013 51.8593 1 1 127 1378295 1268519
1 kirby127a_3_1_ax.img Telencephalon_R 543404 0.0 300.0 135.0683 53.6471 1 1 127 1378295 1268519
2 kirby127a_3_1_ax.img Diencephalon_L 9683 15.0 295.0 193.5488 32.2733 1 1 127 1378295 1268519
3 kirby127a_3_1_ax.img Diencephalon_R 9678 10.0 335.0 193.7051 32.7869 1 1 127 1378295 1268519
4 kirby127a_3_1_ax.img Mesencephalon 10268 55.0 307.0 230.8583 29.2249 1 1 127 1378295 1268519
In [4]:
brain_t1l1 = brain_d.loc[(brain_d.type == 1) & (brain_d.level == 1)]
vol_t1l1 = brain_t1l1.groupby(brain_t1l1.roi).agg(volume=("volume", "sum")).reset_index()
vol_t1l1
Out[4]:
roi volume
0 CSF 1761614
1 Diencephalon_L 180118
2 Diencephalon_R 181723
3 Mesencephalon 206457
4 Metencephalon 2979968
5 Myelencephalon 90339
6 Telencephalon_L 10027994
7 Telencephalon_R 10194129
In [5]:
label = ["ICV"] + list(vol_t1l1.roi)
source = [0]*len(vol_t1l1)
target = np.arange(1,9)
value = list(vol_t1l1.volume)

fig = go.FigureWidget(data=[go.Sankey(
    node = dict(
      pad = 15,
      thickness = 20,
      line = dict(color = "black", width = 0.5),
      label = label
    ),
    link = dict(
      source = source,
      target = target,
      value = value
  ))])

fig.show()